A Google Summer of Code project about NotifyOSD notification was recently brought up for discussion in the Ayatana mailing list. Unfortunately Mark Shuttleworth dismissed almost all the ideas related to NotifyOSD's behavior.

Mark agrees making a GUI you can use to set up the persistence time, UI modifications over a basic structure, font size/style, but that's it.

Here's what Mark Shuttleworth says about 'stacking' (make the bubbles dock downwards as they are initiated and start to stack up as the bubble times finish away) or a close button on NotifyOSD:

Please, no. I would urge Mirco NOT to take patches that introduce that sort of behaviour. We are trying to build clean and tested codebases, and the more alternative pathways we support, the less maintainable it becomes.

The design experience of Notify-OSD is what it is. Changing the style is one thing, changing the behaviour of the bubbles is another thing entirely. We are just NOT going to support simultaneous display, the design is queued and serialized.

So it seems the patched NotifyOSD we were telling you about a few days ago is the closest thing we're going to get for a customizable NotifyOSD (since the changes he agrees on are mostly covered by the patched NotifyOSD). But maybe someone will patch NotifyOSD even further (hint if you're a developer =) ).